## Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
##   object 'config' not found

Project info

Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only)

Filtering samples: C6_2h_3 & PC-12_8h_3

Only those reads were counted, where LoRTIA found both 5- and 3-prime adapters!

Correct some genes in the annotation

DO NOT Filter second copies of genes, as in some cases there are transcripts from only one of the copies

Counts based on iterative GFF-compare results

This was done as follows:

  1. The reference transcripts were compared individually/iteratively to the reads.

  2. The distances between the reads and each reference transcript hit were calculated.

  3. For each read, the most similar reference transcript was assigned (lowest distance).

  4. Additionally, these distances must had fulfill the following rules: max prime5 distance <= 10
    max prime3 distance <= 10
    exon/intron junction difference <= 2

  5. Thus based on these, the read counts for each reference transcript were assessed.

  6. The transcripts were then assigned to their parent genes (by Torma G) and their ratio (isoform ratio) was calculated as follows:
    isoform ratio = transcript isoform count / total gene count

  7. Those reads that could not be assigned to the reference transcripts were assigned to their parent genes, based on their 5-prime ends and independently to their parent gene cluster, based on their 3-prime ends.
    So the reads are either:

  • assigned to a reference transcript
  • could not not be assigned to a ref TR, in which case they were:
    1. assigned to their parent gene based on their 5-prime end overlapping with the gene’s TSS
    2. assigned to their parent gene-cluster based on their 3-prime end overlapping with the cluster’s TES
    3. assigned to both

1. Kinetics of Reference Transcript Isoforms, according to their host gene

The reads were assigned to their parent gene based on their 5-prime end overlapping with the gene’s TSS
(but not necessarily with the gene cluster’s TES)

## NULL

Merge annotation with RefClass

Exclude those ref transcripts that were not observed (or observed under the threshold) from the annotation as well

Evaluate CAGE against dcDNA read counts

## Key: <transcript_id>
## Empty data.table (0 rows and 36 cols): transcript_id,CAGE_ID,score,support,CAGE_significance,seqnames...

##        gene     N
##      <char> <int>
##  1:     CTO  7799
##  2:    NOIR 10766
##  3:    ORF1  3004
##  4:   ORF10  2242
##  5:   ORF11 13394
##  6:   ORF12  7041
##  7:   ORF13  1437
##  8:   ORF14 17457
##  9:   ORF19  9218
## 10:   ORF23  6801
## 11:   ORF24  8431
## 12:   ORF28   479
## 13:   ORF27  1650
## 14:   ORF29  3365
## 15:    ORF3  3585
## 16:   ORF31  3707
## 17:   ORF32  7141
## 18:   ORF33  3100
## 19:   ORF34 13265
## 20:   ORF38  8266
## 21:   ORF39  6484
## 22:    ORF8  5526
## 23:   ORF40  5624
## 24:   ORF41   550
## 25:   ORF42 13205
## 26:   ORF43 30295
## 27:   ORF45   551
## 28:   ORF46  7027
## 29:   ORF48   560
## 30:   ORF49  1797
## 31:   ORF50  2420
## 32:   ORF51  5714
## 33:   ORF53  7564
## 34:    <NA> 21256
## 35:   ORF54 10621
## 36:   ORF57  8358
## 37:   ORF58 31916
## 38:   ORF64 11121
## 39:   ORF65 18521
## 40:   ORF66  3046
## 41:   ORF67 19946
## 42:   ORF69   844
## 43:   ORF70  4555
## 44:   ORF71 11767
## 45:   ORF72  2719
## 46:   ORF73  6459
## 47:   ORF74  1269
## 48:   ORF75  3872
## 49:   ORF76   769
## 50:   ORF17  4701
## 51:   ORF35  3083
## 52:   ORF15  9679
## 53:    ORF9 11057
## 54:   ORF16  3220
## 55:   ORF18 12641
## 56:    ORF2  4130
## 57:   ORF20  8207
## 58:   ORF21  1072
## 59:   ORF22 11355
## 60:   ORF25  6854
## 61:   ORF26  1861
## 62:   ORF30  5787
## 63: ORF35.5  5778
## 64:   ORF36  4161
## 65:   ORF37  2706
## 66:    ORF4  1933
## 67:   ORF44  8836
## 68:    ORF5  6844
## 69:   ORF52 12355
## 70:   ORF55  3656
## 71:   ORF56   853
## 72:   ORF59 10235
## 73:    ORF6  1713
## 74:   ORF60  3352
## 75:   ORF61   947
## 76:   ORF62  2723
## 77:   ORF63  9807
## 78:   ORF68  1737
## 79:    ORF7   239
##        gene     N
##      gene class_code     N
##    <char>     <char> <int>
## 1:   <NA>          =    58
## Key: <gene>
##        gene 3`-long 3`-short 5`-long 5`-short     = Splice-variant     c     e
##      <char>   <int>    <int>   <int>    <int> <int>          <int> <int> <int>
##  1:    <NA>     207      256      59      309    58             14   388     2
##  2:     CTO      93       61    1790     2085   424            681    85    NA
##  3:    NOIR     166       62    1522      784   531            123   388  1645
##  4:    ORF1      12       97     534     1237   159             79    79    NA
##  5:   ORF10      32      228     145      755   221             81   130    NA
##  6:   ORF11     115      450    1883     6530   660            207   957    NA
##  7:   ORF12      59      451     382     3904   238            140   619    NA
##  8:   ORF13       2      448      48      148   122            402    17    NA
##  9:   ORF14       5      907    2739     4325   412            281  2780    NA
## 10:   ORF15      20      970    3282     3008   355            255   327    NA
## 11:   ORF16      11      983     182      773   419            356    79    NA
## 12:   ORF17      90      133     154     2397   145              7   293    NA
## 13:   ORF18      45      428    3288     3110   419            491   296    NA
## 14:   ORF19       3      154    1015     6090   350            131   518    NA
## 15:    ORF2       8      140     350     2617   206             23   400    NA
## 16:   ORF20       3      257    1374     4928   195             76   540    NA
## 17:   ORF21       3      148      64      357   121             70    60    NA
## 18:   ORF22      19      423     587     7926   325            210   429    NA
## 19:   ORF23      15      189    1888     2630   209             48   287    NA
## 20:   ORF24      21      107    1586     3128   246             44   852    NA
## 21:   ORF25      94      921    1121     2703   287            501   260    NA
## 22:   ORF26       2       84     307      870   131             23    94    NA
## 23:   ORF27       5       23     175      270    58             11   100    NA
## 24:   ORF28      NA       28      34      168    45             13    40    NA
## 25:   ORF29      37      513     529     1399   190            119   135    NA
## 26:    ORF3       5       88     390     2552   133             29   147    NA
## 27:   ORF30       2       55    1766     1652   184             47    74    NA
## 28:   ORF31       4      872     216     1273   178            276   331    NA
## 29:   ORF32      13       89     119      965   101             11   197    NA
## 30:   ORF33      31      296     111     1166   259            194   622    NA
## 31:   ORF34      24      464     486     4611   292            199   574    NA
## 32:   ORF35       4        9     333      673    34              9    40    NA
## 33: ORF35.5      33      805     510     2464   237            241   517    NA
## 34:   ORF36      32      263     259     2265   188             73   394    NA
## 35:   ORF37      17       65     420     1128   157             40   108    NA
## 36:   ORF38       2      129     905     5330   463             97   440    NA
## 37:   ORF39      32       77    2500     1878   201             61   334    NA
## 38:    ORF4       4       70     371     1088   142              8    57    NA
## 39:   ORF40      28      545     359     2279   334            307   452    NA
## 40:   ORF41       2      149      59       35   103             40    20    NA
## 41:   ORF42      67     3804     182     1625   383           1650  1878    NA
## 42:   ORF43      73     1577    2266     6919   466            235  9213    NA
## 43:   ORF44       3      115    2157     2746   476             54   117    45
## 44:   ORF45      NA       75      93       81   110             72    11    NA
## 45:   ORF46       8      199     596     4510   156             45   414    NA
## 46:   ORF48       2       68      52      162   151             45     7    NA
## 47:   ORF49       2       24     165      373    77             15   114    NA
## 48:    ORF5       4      201     705     4755   197             67   358    NA
## 49:   ORF50       1      168     289     1195   179             33   227    NA
## 50:   ORF51      12      142    3321      827   206             14    45    NA
## 51:   ORF52       5      550     478     7450   263            431  1147    NA
## 52:   ORF53      37      123     115      196   138             27  1921  1265
## 53:   ORF54     576     1152     637     4288   483            496  1526    NA
## 54:   ORF55      14       35    1046      723    92              7   154    NA
## 55:   ORF56       2       27      29       80    54             19    52    NA
## 56:   ORF57      39      260    1840     2039   547             24  1069    NA
## 57:   ORF58      12     1415    7693    11551  1099            796  1126    NA
## 58:   ORF59      47      788    1071     5297   459            338   910    NA
## 59:    ORF6       6      547     231      252   202            158    53    NA
## 60:   ORF60      10      578     700      785   375            396   105    NA
## 61:   ORF61       2      199     183      172    96             59    54    NA
## 62:   ORF62       3      877      94      325   180            327   103    NA
## 63:   ORF63       1      384     501     4870   133            293  1425    NA
## 64:   ORF64      NA      144      30     6617    46             64  1278    NA
## 65:   ORF65      46     2643    3775     4989  1460           2003   392     9
## 66:   ORF66       6      130     452     1640   184             24    74    NA
## 67:   ORF67      14     1268    1196    10435   384            533  3374    NA
## 68:   ORF68      NA      193     212      419   111            119   182    NA
## 69:   ORF69      28      126      92       55    67             72    63    NA
## 70:    ORF7      NA        1      35      107    20              5     6    NA
## 71:   ORF70      51      111     418     2472   188             52   248    NA
## 72:   ORF71      29      745    2299     3021   287            104   821    NA
## 73:   ORF72      16      124     455      684   209            113    38    NA
## 74:   ORF73       2      113     767     3700   111             26   664    NA
## 75:   ORF74      27       33      37      600    95             30   123    NA
## 76:   ORF75      30      211     473     2403   189             91    92    NA
## 77:   ORF76      NA      140      45      191    97             86    66    NA
## 78:    ORF8      10      218    1153     2770   296             62   216    NA
## 79:    ORF9      17      185     682     2008   272             73   359    NA
##        gene 3`-long 3`-short 5`-long 5`-short     = Splice-variant     c     e
##         i     j     k     m     n     o     p     x     y     ~
##     <int> <int> <int> <int> <int> <int> <int> <int> <int> <int>
##  1:    NA    18    69    12    NA  1007   281 18475    13    88
##  2:    NA    NA   167    NA    NA   479    22  1855    NA    57
##  3:    NA   155   154  1276   254  2043    35   522   618   488
##  4:    NA    NA   294    NA    NA   353    NA    93     2    65
##  5:    NA    NA     2    NA    NA   205    NA   244    NA   199
##  6:    NA    NA    34    NA    NA   742    87   828    NA   901
##  7:    NA    NA     9    NA    NA   507     9   518    NA   205
##  8:    NA    NA    NA    NA    NA   170    NA    67    NA    13
##  9:    NA    NA   233    NA    NA  2655    NA  2682    NA   438
## 10:    NA    NA   141    NA    NA   662    NA   242    NA   417
## 11:    NA    NA     2    NA    NA   208    NA   143    NA    64
## 12:    NA    NA    59    NA    NA   171   302   679     1   270
## 13:    NA    NA   350    NA    NA  2311    36  1620    NA   247
## 14:    NA    NA     3    NA    NA   559    NA   258    NA   137
## 15:    NA    NA     5    NA    NA    87    46   138    NA   110
## 16:    NA    NA    12    NA    NA   435    13   226    NA   148
## 17:    NA    NA     2    NA    NA    65    NA   166    NA    16
## 18:    NA    NA    11    NA    NA   840    37   461     1    86
## 19:    NA    NA   135    NA    NA   411   237   574    NA   178
## 20:    NA    NA   284    NA    NA   535   147  1313     2   166
## 21:    NA    NA    66    NA    NA   320    32   406    NA   143
## 22:    NA    NA     2    NA    NA   132    NA   165    NA    51
## 23:    NA    NA    36    NA    NA   144    31   777     1    19
## 24:    NA    NA     2    NA    NA    30    NA   113    NA     6
## 25:    NA    NA    39    NA    NA   251    NA    83    NA    70
## 26:    NA    NA    12    NA    NA    81    NA    58    NA    90
## 27:    NA    NA    59    NA    NA   381    NA  1466    NA   101
## 28:    NA    NA     5    NA    NA   211    NA   323    NA    18
## 29:    NA    NA     9    NA    NA   112    15  5467    NA    43
## 30:    NA    NA    NA    NA    NA   187    NA   180    NA    54
## 31:    NA    NA    15    NA    NA   426    96  5933     1   144
## 32:    NA    NA    12    NA    NA   300     8  1605    NA    56
## 33:    NA    NA     4    NA    NA   633    NA   208    NA   126
## 34:    NA    NA     3    NA    NA   150    NA   454    NA    80
## 35:    NA    NA    11    NA    NA   305    54   306    NA    95
## 36:    NA    31     3    15     1   150    42   472    27   159
## 37:    NA    NA   351    NA    NA   185    NA   609    NA   256
## 38:    NA    NA    12    NA    NA    34    NA    84     1    62
## 39:    NA    NA     6    NA    NA   589     1   564    22   138
## 40:    NA    NA    NA    NA    NA    76    NA    60    NA     6
## 41:    NA    NA     1    NA    NA  1323    NA  2196    NA    96
## 42:    NA    NA    35    NA    NA  2798   133  6077     2   501
## 43:     8   143    50   696    12    70    22  1895    13   214
## 44:    NA    NA    NA    NA    NA    75    NA    27    NA     7
## 45:    NA    NA    17    NA    NA   383   129   499    NA    71
## 46:    NA    NA    NA    NA    NA    29    NA    29    NA    15
## 47:    NA    NA    26    NA    NA   203   181   595    NA    22
## 48:    NA    NA    NA    NA    NA   317    NA   158    NA    82
## 49:    NA    NA     3    NA    NA   142    NA   136    NA    47
## 50:    NA    NA   407    NA    NA   296    33   343    NA    68
## 51:    NA    NA     1    NA    NA  1027    NA   714    NA   289
## 52:    20     9     4  2644     1   515    37   475    NA    37
## 53:    NA   216    63    NA    14   350    NA   334    NA   486
## 54:    NA    NA    80    NA    NA    90    NA  1369    NA    46
## 55:    NA    NA     3    NA    NA    17    NA   559    NA    11
## 56:    NA    NA   137    NA    NA   716     3  1204    NA   480
## 57:   134   571   436    86   141  3460     4  1133    70  2189
## 58:    NA    NA     2    NA    NA   623    NA   265    NA   435
## 59:    NA    NA     1    NA    NA    96    NA   139    NA    28
## 60:    NA    NA     2    NA    NA   232    NA    88    NA    81
## 61:    NA    NA    NA    NA    NA    86    NA    73    NA    23
## 62:    NA    NA    33    NA    NA   548    NA   210     1    22
## 63:    NA    NA     8    NA    NA  1622    90   418     1    61
## 64:    NA    NA    NA    NA    NA   960   189  1779    NA    14
## 65:    NA   205    26   133     5   809     8  1162     4   852
## 66:    NA    NA     8    NA    NA   102     6   368    NA    52
## 67:    NA    NA    99    NA    NA  1516    NA   259     2   866
## 68:    NA    NA     2    NA    NA   400    NA    62     1    36
## 69:    NA    NA     4    NA    NA    66    NA   250    NA    21
## 70:    NA    NA    NA    NA    NA    51    NA     2    NA    12
## 71:    NA    NA    35    NA    NA   312   273   322    NA    73
## 72:    NA    NA   265    NA    NA   523    NA  3482    NA   191
## 73:    NA    NA   193    NA    NA   357     1   438     6    85
## 74:    NA    NA     9    NA    NA   665    NA   227    NA   175
## 75:    NA    NA     7    NA    NA    85    NA   178     1    53
## 76:    NA    NA    14    NA    NA   163    45   128    NA    33
## 77:    NA    NA    NA    NA    NA    66    NA    69     1     8
## 78:    NA    29    36    NA    NA   182    NA   448    47    59
## 79:     2   119    46    20     5   731     9  6398    45    86
##         i     j     k     m     n     o     p     x     y     ~

There are many transcripts that were identifed with CAGE, and have a high read count in the dcDNA but are novel (not in the reference). They are not the product of false 5-prime sites as they have correct TSS adapaters. Most of these are antisense or 5-prime short but there are 5-prime longs (both shere the 4-primes with ref transcripts) and ‘c’ as well (which have different 3-primes)

Lets check them gene-wise The 5-prime long and short variants.

It seems that ORF51 particularly has a lot of these Check the novel long isoforms for this gene first

Select TSS clusters that are significant (non-NA) in the CAGE results AND have sufficient read counts in the dcDNA reads as well, from where their 5-prime ends were correct and their class-code based on gff-compare was either 5-prime short or long.

Exclude those transfrags that have more than one exon, for now.

## [1] 10837
## [1] 252
##  [1]  954 1224 2246 2261 3011 3014 3327 4014 3344 3394 3458 2228 3385   96  132
## [16]  134  166  193  413  415  657  687  704  725  805 1105 1354 1477 1496 1715
## [31] 1733 2337 3343 1004 2714  275  313  400  500  644  771  878 1027 1542 1894
## [46] 2185 2308
## [1] FALSE
## [1] TRUE
##     CAGE_cluster_width      N
##                  <num>  <int>
##  1:                  1   4564
##  2:                  2    654
##  3:                  3   1624
##  4:                  4   1983
##  5:                  5   1117
##  6:                  6   7498
##  7:                  7   3975
##  8:                  8   1624
##  9:                  9   3108
## 10:                 10   1983
## 11:                 11   1174
## 12:                 12   1129
## 13:                 13   2358
## 14:                 14   1176
## 15:                 15   1114
## 16:                 16   1473
## 17:                 17   1533
## 18:                 18   1059
## 19:                 19   1010
## 20:                 20    983
## 21:                 21    714
## 22:                 22    412
## 23:                 23    551
## 24:                 24    453
## 25:                 25   1416
## 26:                 26   1443
## 27:                 27   1072
## 28:                 28    202
## 29:                 29   1017
## 30:                 30    229
## 31:                 31   1437
## 32:                 32   1539
## 33:                 33   1385
## 34:                 34   3477
## 35:                 35   1048
## 36:                 36    984
## 37:                 37   2146
## 38:                 38   3796
## 39:                 39   3981
## 40:                 40    232
## 41:                 41    236
## 42:                 42   1638
## 43:                 43   1602
## 44:                 44    635
## 45:                 45    727
## 46:                 46     21
## 47:                 48    603
## 48:                 51   1433
## 49:                 52    202
## 50:                 53    646
## 51:                 54   1040
## 52:                 55   1943
## 53:                 57   2361
## 54:                 59    607
## 55:                 60    385
## 56:                 65    902
## 57:                 67    573
## 58:                 70   1444
## 59:                 72   1102
## 60:                 74    260
## 61:                 77   3796
## 62:                 78   6256
## 63:                 82   1795
## 64:                 86    932
## 65:                 90    874
## 66:                128    496
## 67:                170   5018
## 68:                222   2305
## 69:                231   4432
## 70:                 NA 425089
##     CAGE_cluster_width      N

## [1] 576
##          seqnames strand      TX_nov_ID sum_count
##            <char> <char>         <char>     <int>
##    1: NC_001491.2      +  TX_nov_ID_103       315
##    2: NC_001491.2      +  TX_nov_ID_715       644
##    3: NC_001491.2      +  TX_nov_ID_720       541
##    4: NC_001491.2      +  TX_nov_ID_721       437
##    5: NC_001491.2      +  TX_nov_ID_614        92
##   ---                                            
## 1250: NC_001491.2      - TX_nov_ID_1026         1
## 1251: NC_001491.2      -  TX_nov_ID_857         1
## 1252: NC_001491.2      -  TX_nov_ID_926         1
## 1253: NC_001491.2      - TX_nov_ID_1222         1
## 1254: NC_001491.2      -  TX_nov_ID_982         1
##        transcript_id       Ref_Class   gene gene_cluster gene_region
##               <char>          <char> <char>       <char>      <char>
##   1:           CTO-L           CTO-L    CTO          CTO         CTO
##   2:           CTO-S           CTO-S    CTO          CTO         CTO
##   3:        CTO-S-AS        CTO-S-AS    CTO         <NA>         CTO
##   4:  NOIR-2-canonic  NOIR-2-canonic   NOIR         NOIR        NOIR
##   5:    NOIR-Canonic    NOIR-Canonic   NOIR       NOIR_1      NOIR_1
##  ---                                                                
## 580:   nct65-Canonic   nct65-Canonic  ORF65      ORF65_1     ORF65_1
## 581:      nct65-Long      nct65-Long  ORF65      ORF65_1     ORF65_1
## 582:     nct65-Short     nct65-Short  ORF65      ORF65_1     ORF65_1
## 583: nct65.1-Canonic nct65.1-Canonic  ORF65        ORF65       ORF65
## 584:    nct65.1-Long    nct65.1-Long  ORF65        ORF65       ORF65
##         seqnames strand exon_number start.TR end.TR start.exon end.exon  start
##           <char> <char>       <int>    <int>  <int>      <int>    <int>  <int>
##   1: NC_001491.2      -           1    73834  74257      73834    74257  73834
##   2: NC_001491.2      -           1    73834  74183      73834    74183  73834
##   3: NC_001491.2      +           1    73856  74182      73856    74182  73856
##   4: NC_001491.2      -           1   143303 144282     143303   144282 143303
##   5: NC_001491.2      +           1   118878 119857     118878   119857 118878
##  ---                                                                          
## 580: NC_001491.2      +           1   122066 122451     122066   122451 122066
## 581: NC_001491.2      +           1   121788 122451     121788   122451 121788
## 582: NC_001491.2      +           1   122258 122451     122258   122451 122258
## 583: NC_001491.2      -           1   140709 141094     140709   141094 140709
## 584: NC_001491.2      -           1   140709 141372     140709   141372 140709
##         end prime5.TR prime5.ex prime3.TR prime3.ex last_exon      source
##       <int>     <int>     <int>     <int>     <int>    <lgcl>      <char>
##   1:  74257     74257     74257     73834     73834      TRUE Torma_et_al
##   2:  74183     74183     74183     73834     73834      TRUE Torma_et_al
##   3:  74182     73856     73856     74182     74182      TRUE Torma_et_al
##   4: 144282    144282    144282    143303    143303      TRUE Torma_et_al
##   5: 119857    118878    118878    119857    119857      TRUE Torma_et_al
##  ---                                                                     
## 580: 122451    122066    122066    122451    122451      TRUE Torma_et_al
## 581: 122451    121788    121788    122451    122451      TRUE Torma_et_al
## 582: 122451    122258    122258    122451    122451      TRUE Torma_et_al
## 583: 141094    141094    141094    140709    140709      TRUE Torma_et_al
## 584: 141372    141372    141372    140709    140709      TRUE Torma_et_al
##      CAGE.cluster.start CAGE.cluster.end           CAGE_ID support       score
##                   <int>            <int>            <char>   <int>       <num>
##   1:              74257            74257 CAGE_cluster_1531       3    414.7285
##   2:              73985            74215 CAGE_cluster_1530       9 196155.6857
##   3:                 NA               NA                        NA          NA
##   4:             144255           144308 CAGE_cluster_1896       9  24468.6633
##   5:             118852           118905  CAGE_cluster_835       9  24468.6633
##  ---                                                                          
## 580:             121909           122130  CAGE_cluster_860       8  12115.5339
## 581:             121767           121848  CAGE_cluster_858       8   6916.8878
## 582:             122244           122310  CAGE_cluster_862       9  12391.8990
## 583:             141030           141251 CAGE_cluster_1871       8  12115.5339
## 584:             141312           141393 CAGE_cluster_1873       8   6916.8878
##      CAGE_significance thick.start thick.end
##                 <char>       <int>     <int>
##   1:                **       74257     74257
##   2:               ***       74183     74183
##   3:                            NA        NA
##   4:               ***      144282    144282
##   5:               ***      118878    118878
##  ---                                        
## 580:               ***      121935    121935
## 581:               ***      121783    121783
## 582:               ***      122259    122259
## 583:               ***      141225    141225
## 584:               ***      141377    141377
##             cmp_ref    seqnames strand   gene      sample gene_region
##              <char>      <char> <char> <char>      <char>      <char>
##     1: NOIR-Canonic NC_001491.2      +   NOIR EHV-1_12h_1      NOIR_1
##     2: NOIR-Canonic NC_001491.2      +   NOIR EHV-1_12h_2      NOIR_1
##     3: NOIR-Canonic NC_001491.2      +   NOIR EHV-1_12h_3      NOIR_1
##     4: NOIR-Canonic NC_001491.2      +   NOIR EHV-1_18h_1      NOIR_1
##     5: NOIR-Canonic NC_001491.2      +   NOIR EHV-1_18h_2      NOIR_1
##    ---                                                               
## 12848:          as9 NC_001491.2      -   ORF9  EHV-1_6h_2        ORF9
## 12849:          as9 NC_001491.2      -   ORF9  EHV-1_6h_3        ORF9
## 12850:          as9 NC_001491.2      -   ORF9  EHV-1_8h_1        ORF9
## 12851:          as9 NC_001491.2      -   ORF9  EHV-1_8h_2        ORF9
## 12852:          as9 NC_001491.2      -   ORF9  EHV-1_8h_3        ORF9
##        Kinetic_class    Ref_Class class_code read_count    hpi  Time cell_line
##               <fctr>       <char>     <char>      <int> <fctr> <int>    <fctr>
##     1:       unknown NOIR-Canonic          =         82    12h    12     RK-13
##     2:       unknown NOIR-Canonic          =         55    12h    12     RK-13
##     3:       unknown NOIR-Canonic          =         61    12h    12     RK-13
##     4:       unknown NOIR-Canonic          =         26    18h    18     RK-13
##     5:       unknown NOIR-Canonic          =         20    18h    18     RK-13
##    ---                                                                        
## 12848:             L          as9          =          0     6h     6     RK-13
## 12849:             L          as9          =          0     6h     6     RK-13
## 12850:             L          as9          =          0     8h     8     RK-13
## 12851:             L          as9          =          0     8h     8     RK-13
## 12852:             L          as9          =          0     8h     8     RK-13
##            group gene_cluster parent norm_base
##           <char>       <char> <char>     <num>
##     1: RK-13_12h       NOIR_1   <NA>         1
##     2: RK-13_12h       NOIR_1   <NA>         1
##     3: RK-13_12h       NOIR_1   <NA>         1
##     4: RK-13_18h       NOIR_1   <NA>         1
##     5: RK-13_18h       NOIR_1   <NA>         1
##    ---                                        
## 12848:  RK-13_6h         ORF9   <NA>         1
## 12849:  RK-13_6h         ORF9   <NA>         1
## 12850:  RK-13_8h         ORF9   <NA>         1
## 12851:  RK-13_8h         ORF9   <NA>         1
## 12852:  RK-13_8h         ORF9   <NA>         1
## Key: <sample>
## Index: <transcript_id>
##               sample transcript_id  cmp_ref class_code   gene           CAGE_ID
##               <char>         <int>   <char>     <char> <char>            <char>
##       1: EHV-1_12h_1             2    ORF75   5`-short  ORF75  CAGE_cluster_987
##       2: EHV-1_12h_1             3    ORF15          =  ORF15 CAGE_cluster_1205
##       3: EHV-1_12h_1             3    ORF15          =  ORF15 CAGE_cluster_1205
##       4: EHV-1_12h_1             4  ORF67.1   5`-short  ORF67              <NA>
##       5: EHV-1_12h_1             4  ORF67.1   5`-short  ORF67              <NA>
##      ---                                                                       
## 1291331:  EHV-1_8h_3        538397 ORF14-L4          x  ORF14              <NA>
## 1291332:  EHV-1_8h_3        538401  ORF44.5          x  ORF44              <NA>
## 1291333:  EHV-1_8h_3        538465    ORF14          o  ORF14              <NA>
## 1291334:  EHV-1_8h_3        538469    ORF52   5`-short  ORF52 CAGE_cluster_1624
## 1291335:  EHV-1_8h_3        538479    ORF34          x  ORF34              <NA>
##          CAGE_significance support      score CAGE.cluster.start
##                     <char>   <int>      <num>              <int>
##       1:               ***       7  1903.5173             135914
##       2:               ***       9 21752.1102              21199
##       3:               ***       9 21752.1102              21199
##       4:              <NA>      NA         NA                 NA
##       5:              <NA>      NA         NA                 NA
##      ---                                                        
## 1291331:              <NA>      NA         NA                 NA
## 1291332:              <NA>      NA         NA                 NA
## 1291333:              <NA>      NA         NA                 NA
## 1291334:                **       4   980.0626              94075
## 1291335:              <NA>      NA         NA                 NA
##          CAGE.cluster.end    seqnames strand TR_start TR_end correct_tss
##                     <int>      <char> <char>    <int>  <int>      <lgcl>
##       1:           135939 NC_001491.2      +   135915 136464       FALSE
##       2:            21211 NC_001491.2      -    20380  21209        TRUE
##       3:            21211 NC_001491.2      -    20380  21209       FALSE
##       4:               NA NC_001491.2      +   138461 138877       FALSE
##       5:               NA NC_001491.2      +   138461 138877        TRUE
##      ---                                                                
## 1291331:               NA NC_001491.2      -    16999  18170       FALSE
## 1291332:               NA NC_001491.2      +    82705  83094       FALSE
## 1291333:               NA NC_001491.2      +    18235  19534        TRUE
## 1291334:            94076 NC_001491.2      -    93038  94076       FALSE
## 1291335:               NA NC_001491.2      -    65085  65256       FALSE
##          correct_tes count   rep    hpi  Time cell_line     group prime3.TR
##               <lgcl> <int> <int> <fctr> <int>    <fctr>    <char>     <int>
##       1:        TRUE     4     1    12h    12     RK-13 RK-13_12h    136464
##       2:        TRUE   324     1    12h    12     RK-13 RK-13_12h     20380
##       3:        TRUE    56     1    12h    12     RK-13 RK-13_12h     20380
##       4:        TRUE     4     1    12h    12     RK-13 RK-13_12h    138877
##       5:        TRUE     1     1    12h    12     RK-13 RK-13_12h    138877
##      ---                                                                   
## 1291331:       FALSE     1     3     8h     8     RK-13  RK-13_8h     16999
## 1291332:        TRUE     1     3     8h     8     RK-13  RK-13_8h     83094
## 1291333:       FALSE     1     3     8h     8     RK-13  RK-13_8h     19534
## 1291334:        TRUE     1     3     8h     8     RK-13  RK-13_8h     93038
## 1291335:        TRUE     1     3     8h     8     RK-13  RK-13_8h     65085
##          prime5.TR
##              <int>
##       1:    135915
##       2:     21209
##       3:     21209
##       4:    138461
##       5:    138461
##      ---          
## 1291331:     18170
## 1291332:     82705
## 1291333:     18235
## 1291334:     94076
## 1291335:     65256
## [1] 538026
## [1] 112945

## [1] 1254
## [1] 1039
## [1] 785
## [1] 613
## [1] 463
## [1] 315
## [1] 298
##     CAGE_significance support     N
##                <char>   <int> <int>
##  1:                **       3    93
##  2:               ***       3    68
##  3:                **       5    86
##  4:                 *       2   266
##  5:                 *       1   434
##  6:                **       4    84
##  7:               ***       7    47
##  8:               ***       9    80
##  9:               ***       8    43
## 10:               ***       6    53

Annotation plotting function

With annnotation

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Tests